1 Information of relsearch


relsearch is open-source software for screening relatives between query and reference databases. The software is graphical-user-interface written in R language (>= 4.2.0) with GNU General Public License v3.0. It can be applied to autosomal short tandem repeat (STR) markers, Y-STR markers, and mitochondrial DNA sequences commonly used in forensic genetics. For autosomal STR markers, likelihood ratios (LRs) of each query-reference pair are calculated considering mutation and drop-out. For Y-STR markers and mitochondrial DNA sequences, the software investigates the number of inconsistencies between query and reference haplotypes.


2 Getting started


  1. Ensure that R (>= 4.2.0) is installed. It is available from the R Development Core Team website (http://www.R-project.org).

  2. Begin an R session.

  3. Install ‘devtools’ package by using the following command.

install.packages("devtools")
  1. Install ‘relsearch’ package by using the following command.
devtools::install_github("manabe0322/relsearch")
  1. Execute the following commands in R to start GUI.
library(relsearch)
relsearch()


3 Autosomal STR


3.1 Load query database


  1. Press the ‘Load’ button for query database.



  1. Select a .csv file for query database. Format of query database is shown in Fig. 1.


Fig. 1. Format of query database for autosomal STR


Note : format of query database

  • This file must include information regarding ‘Sample Name’ and each marker.

  • There are two columns in each marker.

  • The marker with two empty cells (e.g., vWA of sample ‘Q20’ in Fig. 1) is ignored when calculating the LR.

  • The marker with one empty cell (e.g., D16S539 of sample ‘Q11’ in Fig. 1) can be regarded as allelic drop-out depending on the setting ‘Drop-out of query genotypes’ (see section 3.4).

  • An example file named “str_query_example.csv” is located in the folder ‘examples’.


3.2 Load reference database


  1. Press the ‘Load’ button for reference database.



  1. Select a .csv file for reference database. Format of reference database is shown in Fig. 2.


Fig. 2. Format of reference database for autosomal STR


Note : format of reference database

  • This file must include information regarding ‘Sample Name’, ‘Relationship’, and each marker.

  • There are two columns in each marker.

  • Names of the column ‘Relationship’ relate to those of relationships in the IBD probabilities (see section 3.6).

  • If the relationship is not identified, leave the cell blank. When calculating LRs, all relationships for which the IBD probabilities is defined are considered.

  • The marker with two empty cells is ignored when calculating the LR.

  • The marker with one empty cell or with two same alleles (e.g., D3S1358 of sample ‘R22’ in Fig. 2) is regarded as the homozygotes.

  • An example file named “str_ref_example.csv” is located in the folder ‘examples’.


3.3 Load allele frequencies


  1. Press the ‘Load’ button for allele frequencies.



  1. Select a .csv file for allele frequencies. Format of allele frequencies is shown in Fig. 3.


Fig. 3. Format of allele frequencies for autosomal STR


Note : format of allele frequencies

  • This file must include information regarding ‘Allele’ and each marker.

  • An example file named “str_af_example.csv” is located in the folder ‘examples’.


3.4 Set conditions of calculation


  1. Press the ‘Condition’ button.



  1. Set conditions of ‘Minimum allele frequency’, ‘Drop-out of query genotypes’, and ‘Probability of drop-out’.



Note : Drop-out of query genotypes

  • ‘Not consider’ : When calculating the LR, the marker with one empty cell in a query or reference database is regarded as the homozygote. The marker with two empty cells is ignored (i.e., LR = 1).

  • ‘Consider only in the case that one allele is designated’ : When calculating the LR, the marker with one empty cell in a query or reference database is regarded as both the homozygote (without drop-out) and the heterozygote (with drop-out). The marker with two empty cells is ignored (i.e., LR = 1).

  • ‘Consider also in the case that two alleles in homozygotes are designated’ : When calculating the LR, the marker with two same alleles in a query or reference database is also regarded as both the homozygote (without drop-out) and the heterozygote (with drop-out).


  1. Press the ‘Save’ button.



3.5 Set mutation rates


3.5.1 Edit mutation rates


  1. Press the ‘Mutation rate’ button. Then the window ‘STR mutation’ will be open.



  1. Select a locus to change the mutation rate.



  1. Press the ‘Edit’ button. Then the window ‘Edit a mutation rate’ will be open.



  1. Enter an arbitrary mutation rate.



  1. Press the ‘Save’ button.



3.5.2 Add a locus


  1. Press the ‘Add’ button in the window ‘STR mutation’. Then the window ‘Add a locus’ will be open.



  1. Enter an arbitrary locus name.



  1. Enter an arbitrary mutation rate.



  1. Press the ‘Save’ button.



3.5.3 Delete a locus


  1. Select a locus in the window ‘STR mutation’.



  1. Press the ‘Delete’ button. Then the selected locus will be deleted.



3.6 Set IBD probabilities


Note :

  • When the relationship of each reference profile is not identified, all relationships for which the IBD probabilities is defined are considered when calculating the LR.


3.6.1 Edit IBD probabilities


  1. Press the ‘IBD probabilities’ button. Then the window ‘IBD probabilities’ will be open.



  1. Select a relationship to change the IBD probabilities.



  1. Press the ‘Edit’ button. Then the window ‘Edit IBD probabilities’ will be open.



  1. Enter arbitrary probabilities of IBD = 2, IBD = 1, and IBD = 0.



  1. Press the ‘Save’ button.



3.6.2 Add a relationship


  1. Press the ‘Add’ button in the window ‘IBD probabilities’. Then the window ‘Add a relationship’ will be open.



  1. Enter an arbitrary relationship.



  1. Enter arbitrary probabilities of IBD = 2, IBD = 1, and IBD = 0.



  1. Press the ‘Save’ button.



3.6.3 Delete a relationship


  1. Select a relationship in the window ‘IBD probabilities’.



  1. Press the ‘Delete’ button. Then the selected relationship will be deleted.



3.7 Perform screening


  1. Press the ‘Screening’ button.



  1. Wait until the screening finishes.



3.8 Check the result of screening


  1. After finishing the screening, the result of the screening will be displayed.



Note : Default display

  • All query names

  • All reference names

  • All relationships

  • Likelihood ratio (LR) > 1

  • Descending order of LR


3.8.1 Change the displayed information


  1. Press the ‘Set display’ button. Then the window ‘Set display’ will be open.



  1. Select a query name, a reference name, and a relationship.



  1. Enter the minimum LR.



  1. Press the ‘Set’ button.



3.8.2 Show the result of a query-reference pair in detail


  1. Select a query-reference pair.



  1. Press the ‘Show detail’ button. Then the window ‘STR result in detail’ will be open.



  1. Press the ‘Export’ button to save the displayed data.



3.8.3 Export data


  1. Press the ‘Export displayed data’ to save the displayed data in the tab ‘STR results’.



  1. Press the ‘Export All LRs’ to save all LR values.



4 Y-chromosomal STR


4.1 Load query database


  1. Press the ‘Load’ button for query database.



  1. Select a .csv file for query database. Format of query database is shown in Fig. 4.


Fig. 4. Format of query database for Y-STR


Note : format of query database

  • This file must include information regarding ‘Sample Name’ and each marker.

  • There is one column in each marker.

  • In the marker with more than one allele, each allele must be separated by a comma (e.g., DYS385).

  • The marker with an empty cell (e.g., DYS390 of sample ‘Q10’ in Fig. 4) is regarded as the ‘ignored loci’.

  • An example file named “y_query_example.csv” is located in the folder ‘examples’.


4.2 Load reference database


  1. Press the ‘Load’ button for reference database.



  1. Select a .csv file for reference database. Format of reference database is shown in Fig. 5.


Fig. 5. Format of reference database for Y-STR


Note : format of reference database

  • This file must include information regarding ‘Sample Name’ and each marker.

  • There is one column in each marker.

  • In the marker with more than one allele, each allele must be separated by a comma (e.g., DYS385).

  • An example file named “y_ref_example.csv” is located in the folder ‘examples’.


4.3 Perform screening


  1. Press the ‘Screening’ button.



  1. Wait until the screening finishes.



4.4 Check the result of screening


  1. After finishing the screening, the result of the screening will be displayed.



Note : Default display

  • All query names

  • All reference names

  • Number of inconsistent loci : 0 or 1

  • Number of ignored loci : 0 or 1

  • Ascending order of the number of inconsistent loci and the number of ignored loci


4.4.1 Change the displayed information


  1. Press the ‘Set display’ button. Then the window ‘Set display’ will be open.



  1. Select a query name and a reference name.



  1. Enter the minimum number of inconsistent loci and the maximum number of loci explained by drop-outs.



  1. Press the ‘Set’ button.



4.4.2 Show the result of a query-reference pair in detail


  1. Select a query-reference pair.



  1. Press the ‘Show detail’ button. Then the window ‘Y result in detail’ will be open.



  1. Press the ‘Export’ button to save the displayed data.



4.4.3 Export data


  1. Press the ‘Export displayed data’ to save the displayed data in the tab ‘Y results’.



5 Mitochondrial DNA


5.1 Load query database


  1. Press the ‘Load’ button for query database.


  1. Select a .csv file for query database. Format of query database is shown in Fig. 6.


Fig. 6. Format of query database for mtDNA


Note : format of query database

  • This file must include information regarding ‘Sample Name’, ‘Range’, and ‘Haplotype’.

  • An example file named “mt_query_example.csv” is located in the folder ‘examples’.


5.2 Load reference database


  1. Press the ‘Load’ button for reference database.



  1. Select a .csv file for reference database. Format of reference database is shown in Fig. 7.


Fig. 7. Format of reference database for mtDNA


Note : format of reference database

  • This file must include information regarding ‘Sample Name’, ‘Range’, and ‘Haplotype’.

  • An example file named “mt_ref_example.csv” is located in the folder ‘examples’.


5.3 Perform screening


  1. Press the ‘Screening’ button.



  1. Wait until the screening finishes.



5.4 Check the result of screening


  1. After finishing the screening, the result of the screening will be displayed.



Note : Default display

  • All query names

  • All reference names

  • Shared length > 300

  • Number of inconsistency : 0 or 1

  • Descending order of the shared length

  • Ascending order of the number of inconsistency


5.4.1 Change the displayed information


  1. Press the ‘Set display’ button. Then the window ‘Set display’ will be open.



  1. Select a query name and a reference name.



  1. Enter the minimum shared length and the maximum number of inconsistency.



  1. Press the ‘Set’ button.



5.4.2 Show the result of a query-reference pair in detail


  1. Select a query-reference pair.



  1. Press the ‘Show detail’ button. Then the window ‘mtDNA result in detail’ will be open.



  1. Press the ‘Export’ button to save the displayed data.



5.4.3 Export data


  1. Press the ‘Export displayed data’ to save the displayed data in the tab ‘mtDNA results’.



6 Manage projects


6.1 New project


  1. Select File -> New project.



6.2 Load project


  1. Select File -> Load project.



  1. Select a project file (.RData).


6.3 Save project


  1. Select File -> Save project.